Truth Be Told
by houseofnightfanclub
Summary: Jocelyn worked up the nerve to save her son from Valentine, but to this day she still cringes around him. She knows the truth. Jonathan has always been treated differently than his sister, Clary, and once she starts running off with a mysterious boy named Jace, Jonathan starts asking questions. Will he find out the dark secrets that have been hidden from him? Sebastian's POV in CoB
1. Prologue

**So this is a new story so i would LOVE if you guys reviewed, letting me know what you guys think. :)**

**_In this story, Jocelyn worked up the nerve to save her son from Valentine, but to this day she still cringes and flinches around him. She knows the truth. Jonathan has always been treated differently than his sister, Clary, and once she starts running off with a mysterious boy named Jace, Jonathan starts asking questions. Will he find out what his mother has been hiding from him all this time, what he is, and what he was created to be?_ **

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Prologue:

_Luke's Lake House: 1996_

Jonathan never felt like he belonged. It always seemed like there were secrets his mother was keeping from him. That is why he did this. In _secret_. Plus, he furtively loved the chaos it brought to the house once his mother found out.

Almost every board in this old lake house squeaked, but experience had taught Jonathan where to zig and where to zag in order to sneak around soundlessly. Of course, it had always been a sort of talent that Jonathan had.

The moon was a silvery crescent in the sky. He looked up at it. It was familiar. Jonathan always thought his silvery blonde hair was like the moon and his dark eye were like the night sky.

Even thought the moon lit up the sky, the clouds were doing a good job at keeping the light from reaching the ground. _Good, _Jonathan thought. It was easier sneaking around in the dark anyway and he had always liked the dark.

Even though he was young, Jonathan was strong. He jogged out to the woods, hopped over logs and barely broke a sweat. He liked that he rarely got tired; it made him think of all of the things he could possibly do.

Had put a small knife—that he had stolen from the kitchen—in his belt loop. He pulled it out and started slicing leaves and twigs as he lunged and parried. This was all fun, but it was not what he came out here for.

Branches snapped under the animal's feet and Jonathan's senses heightened, much like an animal himself. Instead of chasing the sound, he stood completely still. He could hear the wind swaying the trees overhead.

The animal drew closer. It was a small deer; its head was down as it fed from some shrubbery. Even though the animal may not know any better, Jonathan held the knife behind his back, out of view. He called it closer with soft clicking noises, his hand held out as if to feed it.

The deer's ears flicked at Jonathan, curious at the creature in front of it. Its shiny nostrils flared as it hesitantly stepped forward.

Jonathan made eye contact with the creature and hoped he was persuading it to come closer.

Soon enough, the deer's soft lips tickled Jonathan's pale palm, searching for food.

Jonathan had to work fast now. No room for error.

His hand moved quickly, flipping the knife so that the blade would plunge into the soft curve of the deer's neck. It didn't take a long time for the deer to die. It bled fast. Jonathan would have like it if the death took longer. He like watching it struggle for breaths. What he liked most was how human it looked when it died, how it seemed to stare into Jonathan's eyes as its life vanished. A smile crept onto Jonathan's face, which was something that didn't happen often.

The blood that was on Jonathan's hands was dark, warm and sticky. He rubbed his fingers together as he felt the texture of it. Even as he walked back to the house he played with the blood as it grew stickier.

Before entering the house Jonathan cleaned off in the lake. Oddly, this lake always reminded him of a mirror, always reflecting the sky. But instead of reflecting the clouds in the sky, a scarlet cloud surrounded his hands as he rinsed off the murder from his hands. He washed the knife and finished up, walking back to the lake house.

Jonathan followed the same trail every time he came out here. _Everything has a pattern_, he thought, _and when it's disrupted_, "Chaos," he said aloud.

Jonathan opened the creaky screen door, but was stopped by a hard body. It plucked the knife from his hand. _Luke. _Luke was the owner of this house. Luke was _not _Jonathan's father, but he was around them practically all of the time. Jonathan didn't have many feelings, but he . . . _tolerated_, Luke. He didn't run away from Jonathan whenever something bad happened like all of the other people in his life—his teachers, his classmates, and sometimes even his mother. Luke was the only thing that Jonathan had for a father, and there was a part of Luke, however small, that was like Jonathan.

"What were you up to, young man?" Luke asked, crossing his arms. Jonathan hated when he was talked down on, like he was a child. _You _are_ a child_, a small voice whispered.

"I was in the woods."

"Doing what?" Luke asked, inspecting the blade. There was a reflection of it on Luke's round glasses, so Jonathan knew that Luke found blood. He rubbed his thumb over a spot Jonathan had missed while cleaning it. "Go back to bed, Jonathan." Luke's voice didn't sound mad. He rarely seemed mad.

His mother would be mad though, but Jonathan never understood why. His mother always seemed mad or frustrated or scared around Jonathan.

Grudgingly, Jonathan made his way up the creaky steps and into the bedroom that he was temporarily sharing with his sister. Even though his late night adventure was invigorating, Jonathan still felt a wave of sleep slip heavily over him. He collapsed onto his bed. The last thing Jonathan saw before he fell asleep was the fiery red of his sister's hair.

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	2. Pandemonium

**Sorry this took long to update. I've been working on two different fics at the same time. I really appreciate all the reviews ;) keep them coming.**

**i forgot to mention earlier that this story will be retelling City of Bones, so i'll try to stick to the story but keep it my own :)**

**also i had two beta readers for the prologue: AND (so a 'thanks' goes out to them)**

**Hope you enjoy this one**

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Chapter 1: Pandemonium

_Present Day (City of Bones)_

"So I've been thinking," Clary started. Jonathan had isolated himself in his room, reading _War and Peace_ when she let herself in with no warning. There was no stopping his sister when she was on a mission and he admired that about her. She was persistent, which is why Jonathan was wary about her starting off her sentence in 'I've been thinking,' He could only imagine what would come next.

Clary had jumped onto Jonathan's bed, making both of them bounce. Clary's red hair fell in a curtain around her as she leaned on her elbows. Jonathan put the huge book down beside him, knowing he would not be able to concentrate while she was talking. "We should go to Pandemonium tonight," Clary said simply. She was picking at the left over polish that was on her nails.

"Pandemonium?" Jonathan arched a pale eyebrow.

"Yeah, you know purple hair, loud music, drunk people grinding on each other…"

"Such a lovely place," He murmured sarcastically.

"I thought you loved that place," Clary asked.

"I do. I just—I've been getting my headaches again lately and they only get worse around Pandemonium and above that, I'd rather _not_ go to a club with my little sister."

"We wouldn't even have to see each other." Clary began to rush her words "We will meet and leave at a certain time. And those headaches are probably just from the loud music. You're tough. You can deal with a tiny headache. Pleeeaase!" Clary begged. Jonathan stayed silent and picked up his book again. "You know mom won't let me go without you. She hates it when I go, and she knows if you go with me that you'll protect me."

Clary was right; he would protect her. If any slime ball had the nerve to even look at her wrong he would make sure they got a left hook in the jaw, possibly (and preferably) until they passed out or found their way to the nearest grave. Any chance Jonathan was given to take his anger out on someone he would take it. Jonathan thought that maybe he could find someone drunk enough to get in a fight with. It was better when they were drunk because they would remember that Jonathan took the first punch. The thought of fighting made him smirk.

"Please Jon, Johnny," Clary smiled wide, knowing he hated those nicknames.

"If you promise never to call me that again," he sighed forebodingly, "I'll go." Jonathan caved. What would one night out hurt?

Jonathan never really liked people. He tolerated some, but never liked anyone. He especially didn't like being around people. He liked isolation. No one judged him here. No one talked behind his back. In school it always seemed like he could hear the whispers and the nasty rumors—which where usually true.

And then there was Clary. He was two years older than her, and they had grown up together. She never was scared of him like the others were; but then again, she didn't know all of the things that made him…_different. _

"Really?!" she cheered. "I'll call Simon and tell him it's a go. Thanks!" Clary got off the bed and walked away.

Jonathan wondered what made him so much different than his sister and mother. Clary was always so happy, and even his mother had her moments, but Jonathan never felt the same joy they felt. He never felt happiness or delight—maybe _pleasure_ a time or two, but never true _happiness_. What made him so different?

Both of them had curly red hair, round faces, freckles, and green eyes while Jonathan lacked _all_ of those qualities. His hair was pale blonde, almost white. His eyes were dark, almost black. His face was blemish free and had hard angles. It made Jonathan wonder what his father was like. His _real _father. Was he like him? Jonathan may never know. His mother had told him that their father had died, but that was it. No pictures. No memorabilia or keepsakes. Jonathan wished that he knew more about him though. He wondered if he was like his father. He wondered if his father was like him. He wondered if his father would understand him.

Jonathan had picked up his book again and continued to read as he heard raised voices battle against each other in the lower level. It sounded like it was his mother and Clary. Jonathan shook his head. A fight between those two was like an immovable force meeting a stationary object. Neither would win.

After the voices stopped he heard feet stomping up the stairs, followed by Clary opening his door again. She looked frustrated, "Ready?"

"Mom was okay with it?"

"Not really," she shrugged, "but I'm going anyway," Clary leaned on the wooden doorframe. Jonathan's mouth twitched in the corner. _Going against mother's wishes?_ Maybe he and his sister were more alike than he thought.

. . .

"You've _got_ to be kidding me." The large bouncer at the club's entrance crossed his thick arms.

Even though Simon, Clary and Jonathan were near the end of the line; they could see a boy with electric blue hair arguing with the man.

Jonathan inspected the boy. He looked normal enough, but something odd stood out, and it wasn't his extra green eyes; a presence of some sort separated him from the crowd. It wasn't his iridescent looks, in fact, he looked just like everyone else here There was something else that most people would find off-putting. It was strange, as Jonathan kept looking at the boy, his headache got worse, forcing his eyes to the ground.

"You thought that boy was cute didn't you?" Simon asked Clary. The two of them had been best friend for as long as Jonathan could remember and he was around just as much as Luke was. Simon tried to be friends with Jonathan as well, but Jonathan never connected. It was the same story with everyone else.

Clary jammed her elbow into Simon's ribs, but said nothing.

. . .

The dimly lit club was full of colorful gyrating bodies. Lights and lasers danced around the room. The smell of dry ice, sweat, and alcohol brought back all of the memories of Pandemonium. Bright hues of pinks, purples and blues bounced on the dance floor. It seemed to have rained glitter by the looks of the floor.

Just as Jonathan predicted, his pulsing headache only got worse inside the club. Clary and Simon were headed to the dance floor and Jonathan grabbed her quickly by the wrist. "I'm going to wait outside," Jonathan shouted over the pulsing music and held out a carton of cigarettes.

"Those things will kill you, you know." Clary looked concerned, but there was still humor in her voice.

"I can take care of myself. Meet me in an hour."

"Kay," Clary said as she pulled Simon into the giant mass of bodies.

Jonathan pushed and maneuvered his way toward the exit. He tried to keep his eyes down, but he snuck a glance every once and a while to make sure he was still on the right path. When he did, he saw a woman with blue eyes, all blue, with no pupil. He assumed she was wearing contacts like the boy in the line, but once she made eye contact, Jonathan's head throbbed again. His breath kept catching in his chest and his pulse raced. What was wrong with him? He didn't like this feeling. This feeling of weakness. Feeling helpless. Jonathan liked being in control.

He picked up his pace and pushed the door that had EXIT written on it. The cool summer air blew around him, clearing his head and clearing his pain.

Jonathan dug his hand into his pocket and grabbed his black lighter, lit his cigarette, and blew the smoke into the night. Immediately, Jonathan felt better; his tense body relaxed. The throbbing ache in his head dulled. In the shadows, he leaned against the cool brick of the club with one leg bent.

He was alone in the ally, apart from a single rat that was picking through some trash. He looked up to the night sky. The moon was high and waxing, but no stars could be seen through the bright city lights. Jonathan always felt better at night. Something about it always brought him to life. The light of day always seemed too harsh to him. There were so many things he couldn't do in the light, but at night…

"Isabelle's in," a boy said. He came from the alley and was talking to a black-haired boy. They must have not seen Jonathan, or have been concerned that he was there, because they carried on their business like he was invisible. The two boys intrigued Jonathan. They were in all black and leather and were covered in peculiar black markings and sprinkled with white scars. Strange clear weapons were strapped to their backs. The blonde one pulled out a knife that had the same strange markings and began to open the door to the club.

Jonathan stepped out of the shadows then. These boys had weapons and they were going into the same club his sister was in. They could wreak all the havoc they wanted, but Jonathan had to get Clary out first.

Jonathan took his hand and pushed the door shut. The handle slipped from the boy's grip. A slight look of shock was plastered on the blonde's face. In fact, both of the boys looked surprised. Jonathan was used to this look. His strength was only another thing that set Jonathan apart from the crowd.

"Nice knife," Jonathan commented, blowing smoke into the boys' faces. The odd looking blade in the blonde's hand seemed to gleam in the moonlight giving it and eerie white glow. Jonathan was about two inches taller than the blonde, but the black haired boy was about Jonathan's height. He could fight _both_ of these boys if he needed to. His strength was superior.

The blonde boy inspected the hilt as if seeing it for the first time again. "Most people don't have… the _eye_ for its beauty,"

"Why do you need it to go clubbing?" Jonathan took another puff of his cigarette; the tip of it glowed deep orange.

"We're on a hunting trip." The blonde smirked.

"Jace," the dark haired boy glanced warily from Jonathan to the other boy, Jace.

"Right, right," Jace seemed to sigh, "We have a job to do, so if you'll excuse us," Jace tried to open the door again, but Jonathan kept it shut—somewhat effortlessly—with his hand. Once again, the boys looked surprised.

"Let me get my sister out first, and then you can kill who ever you want," Jonathan threw his cigarette butt on the alley floor, opened the door, and walked in first.

The club was just as loud as before, but Jonathan's headaches were inexplicably gone. These headaches were peculiar. They had been coming on and off for about a week now, and getting worse in the past few days, but this wasn't the first time this happened. Jonathan could remember getting episodes like this before. They were never bad in his childhood, but as they grew up, they only got worse—so bad that he actually asked his mom for help, which surprisingly helped. The pain would go away and then come back in a few months, and the cycle would repeat. Over and Over.

Through the thick crowd Jonathan couldn't pick out Clary's fiery hair. He couldn't find the two boys from the ally either. The one person he could seem to find was Simon, who seemed to be on a hunt as well. Jonathan stopped Simon in his tracks, grabbing his shoulders. "Simon, where's Clary?" Jonathan yelled over the thunderous music.

"She was talking about some guy with a knife and went parading thru the crowd." Simon used his hands when he talked and pointed to two large men behind him. "I called security."

"Which way did she go?" Jonathan interrogated. Simon pointed to the back of the club towards a door with NO ADMITTANCE written on it in red.

Jonathan moved before Simon could fit in another explanation. He didn't worry about the guards keep up with his swift pace either. He moved thru the crowd like smoke.

He made it to the door just as it opened. Clary stepped out. She looked at Simon and then at Jonathan. "I thought they went in there, but I guess they didn't." The guards went to check the room, but the defeat on Clary's face told Jonathan that she must have lost their trail. Clary clenched her jaw and made eye contact with them then, "let's go home."

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	3. Secrets and Lies

Chapter 2: Secret and Lies

Jonathan poured himself a bowl of cereal, milk and orange juice. He carried it all to the table and sat down. His mother was out with Luke and his sister was talking on the phone with what sounded like Simon, so he sat alone.

Jonathan's eyes wandered around the room as he chewed, until they fell upon the portrait over the fireplace of a man dressed in military gear. This man was Jonathan's father, and no matter how long Jonathan stared at the picture, he could never find a connection with the man on the wall. If Jonathan was nothing like his mother then he was like his father, right? And yet there was nothing in that portrait that made Jonathan feel connected to his father—only that they shared the same name. Jonathan Clark: decorated war veteran. Amusingly, it wasn't a battle that killed him but rather a silly car crash. Jonathan never knew his father; he had died before he was born. Jocelyn never talked about him much either. It only made Jonathan want to know more.

"Hello? Earth to Jonathan," Clary waved her hand in front of his face, snapping him out of his gaze at the portrait.

"What?" he angrily pushed Clary's arm out of his view. He hated when people snuck up on him. It rarely happened, but he still hated it.

She sat down at the round wooden table with him. "You're cranky. Are you hung-over?"

"No." Jonathan snapped. He let his eyes drop to his bowl of cereal.

"Thinking about dad?" She glanced at the portrait now, "You know Mom will never tell us anything." She shifted in her seat, "besides, we have Luke."

Then, almost like clockwork, Luke—a tall, brown-haired man in a flannel shirt and round glasses—walked through the door.

"Hey, Luke!" Clary said cheerfully. "Where's Mom?"

Luke shut the door with his foot since his hands were full with a boxful of pasteboard. Jonathan said nothing to acknowledge Luke and scooped up another spoonful of cereal. "She's out parking the truck. Remind me again why this old apartment doesn't have an elevator."

"Because it's _old_," Clary raised an eyebrow.

"What's with the boxes anyway?" Jonathan asked, curious now. They had never moved, but they do go to Luke's summerhouse, generally it's because of Jonathan. Six weeks ago Jonathan beat a man unconscious at Pandemonium for trying to take away the girl he was dancing with. So they went to the farmhouse for a week. His mom always said it gave them a chance to 'breathe' or to 'cool off'. Neither Luke, nor Jocelyn, nor Jonathan said anything to Clary. Jonathan assumed this was another trip, but he couldn't remember doing anything wrong.

"Just packing up extra things," Luke explained. He made eye contact with Jonathan sending a silent message. They weren't going to the lake house because of him. This was different.

"Hey, Luke?" Clary asked. She twirled a red curl around her finger; it was a nervous habit she had. "What would you do if you saw something no one else did?"

Luke dropped a roll of packing tape. When he bent to pick it up he refused to make eye contact with her, but he glanced quickly at Jonathan. "Like a crime or something?"

Jonathan was confused too. What was Clary concerned about? Was this about last night? _Did _she witness those two boys murder someone? Had she seen Jonathan do something that other people frown upon?

"No. Look, I know it sounds crazy, but what if there were other people around, but you were the only one who could see something. As if it were invisible to everyone but you."

Both Luke and Jonathan looked at her. Luke's face was tight while Jonathan's held confusion. "You must have been the one drinking last night, not me," he forced a smile. Jonathan never smiled as a child. He remembered his mother and Luke telling him to do it more often and when he asked why they said it was the 'normal' thing to do. Even then they knew he wasn't ordinary.

Quickly Jonathan's fake smile faded when he remembered seeing the girl with all blue eyes. Had Clary seen her too? Were there other people out there that Clary could see too?

Clary shot Jonathan an angry look, "You're the one that had the headaches, not me,"

Luke blue eyes glanced at Jonathan over his glasses. "You've been having headaches again?" Jonathan shrugged. "You promised to tell us when they came up again,"

"Guess I've had other priorities," Jonathan grabbed his bowl and tossed it in the sink where it clattered to the bottom.

"Jonathan!" Jocelyn yelled as she came through the door. She took a forced centering breath—this happened often when she talked to her son. It's like she tried to calm herself so that Jonathan's anger would grow. Jonathan guessed it was logical thinking. His anger could get out of control quite easily and having someone yelling at him didn't help. "You're going to break the dishes if you keep doing that." She set the truck's keys on the table as she joined the conversation.

"Mom," Clary asked, "What are the boxes for?"

Jocelyn's mouth was a straight tight line. It seemed Luke had to talk for her, "We're going on a vacation. To the farmhouse,"

Jonathan leaned against the counter, his pale brows furrowed. Why did they keep insisting to go to Luke's house? He couldn't remember doing anything wrong. Of course, it was hard to tell, their perception of wrong and his were two entirely different things. "I haven't done anyth—"

"It's not about you, Jonathan," His mother put up a hand, she seemed flustered.

"It's about last night, then," Clary spoke up, oblivious to Jonathan's comment.

"No." Jocelyn said quickly and then corrected herself, "maybe. You two shouldn't have gone to that club. You know I don't like that place."

"Just tell them, Jocelyn," Luke pleaded.

Their mother pinched the bride of her nose. "Now is hardly the time, Luke," she looked at her children now. "We are just going to the farmhouse for a few weeks until school starts up again," Jocelyn put her hand on her hips. Her red hair fell in front of her eyes. "Okay?"

Before either of them could speak up, she grabbed a box and started packing things from the living room.

"But that's not fair!" Clary yelled across the room. "Simon and I have plans, I have art meetings, and Tisch—"

"I'm sorry, Clary, you can't go. The money is too tight right now,"

"But—" Clary bit her lip. "Luke, tell her it's not fair! She promised I could go." Luke said nothing. "Jonathan? Help me,"

Jonathan said nothing to his sister. Most likely they were going to the farmhouse because of him, because of something he did, something his mother was trying to prevent from happening again.

This was his fault, not Clary's, and yet he didn't say anything. Clary gave an annoyed grunt and stomped up the stairs.

"Luke's right, we should tell her the truth," Jonathan spoke up. His mother looked at him with wide eyes. "Tell her we always go to Luke's because of me. She feels like she's the one being punished,"

"This isn't about you. I just feel like we could use some space,"

Jonathan crossed his muscled arms over his chest, "you keep saying that, and yet, I don't believe you. I'm not as fragile as Clary. I don't care if you punish me for something _you_ think is wrong,"

"Pack your things, Jonathan," It wasn't a request, but an order. Jocelyn's voice was tight.

He rolled his eyes as he walked to the stairwell, and as he reached the top he could hear his mother and Luke bickering, even though he was out of sight. He listened.

"Jonathan said he was getting headaches again." Luke started. "Clary said she saw something unexplainable at Pandemonium," Luke's voice was hushed. "Have you called him?"

His mother spoke softly too. "Three times. It goes to voicemail every time," Jonathan could hear his mom sigh. "It says he's in Tanzania."

"It will be okay. Jonathan's always been harder—" Luke eased Jocelyn's frustration.

"It's not _just_ about Jonathan. I'm afraid _he's_ found me, and if he's found me, then he will find Clary, and Jonathan. I can't let them turn out like their father. He wants Jonathan. I know it. I took Jonathan away and now he wants him back. If he finds Jonathan—"

"I know." Luke's voice always seemed like the clam in the storm. He centered everyone in this house, including Jonathan. "We can leave early tomorrow."

Seeming like the end of the conversation, Jonathan silently retreated to his bedroom. Downstairs, the door flew open. Curious, Jonathan looked to see who it was. Simon. He face held a dopey smile, seeing that he interrupted something. "Did I interrupt something?" He looked at all of the faces in the room. "I can come back,"

Behind Jonathan, Clary came racing down the stairs, her brows furrowed. "Forget it, Simon. We're leaving." Clary grabbed Simon by the wrist and stormed off. Luke shortly followed, leaving Jonathan and his mother together.

Great.

"I get one last day of freedom too, right?" Jonathan asked, not that he cared what she said. He said it more to annoy her. He leaned on the staircase's railing, crossing his arms—his usual pose.

"No. You are going to pack." His mother turned her back, and with shaking hands, began to pack.

. . .

Jonathan didn't know what to do. Usually he would go out, find someone and do what he pleased with him or her, but it was still daylight. Jonathan didn't like going out in the daylight where everything could be seen so clearly. He liked the night, where he could lurk around unseen.

He walked to the edge of his bed, stuffed his hand between the mattresses and pulled out his knife. It gleamed in the ray of sunlight that snuck through the shades. Jonathan smiled faintly at his reflection. He sat on the wooden chest at the end of his bed. He let the knife twirl in his hand. It seemed like a normal habit he had. He did it whenever he was stuck inside the awful apartment, which was most times, considering he didn't have any friends and refused to 'have fun' in the daylight.

He flung the knife at the wall where a corkboard was strung up. _Thump._

A few hours had gone by. Jonathan sat in his room, repeating the motion over and over and over. His mother never bothered to come in and see what the noise was. _Because she's afraid of you_, a voice said, _she knows what you really want to do at night_. She knows you want to murder. She knows you want to see the fear in a man's eyes as you take his life, hear the plea for his life, feel his heartbeat slowly and painfully come to an end.

Ironically, Jocelyn seemed to be the only one who really _knew_ Jonathan despite their lack of interaction. For a moment, Jonathan actually thought about how much he tolerated his family, more than most people. He always thought about what damage could be done to other people, but not his family. They were the few people he…_rarely_ thought about hurting.

There was a crash downstairs, followed by books falling, feet stomping and a loud thud. He heard his mother scream. For a moment, he thought that he was just hearing the things he liked to hear. Fear. Pain. Torment. But it was real. His mother was in trouble.

"_Where is it_!" a male's voice, that Jonathan didn't recognize, yelled. There was another bang, and then silence.

With the knife in his hand he ran down the stairs, two at a time, completely silent. Once he reached the main level he saw the mess that had been made. All of Jocelyn's paintings had been slashed, their frames broken. The floor was a mess. It looked like a hungry monster had broken in, fed, and left all of this chaos as its scraps.

The cabinet's contents were spilling out onto the floor. The vanity and its drawers were completely destroyed.

Jonathan stepped on papers and old art tools, but he wasn't the only thing slithering around. Jonathan turned around to see a long, scaled creature with a cluster of flat black eyes set in the front of its domed skull. Something like a cross between an alligator and a centipede, it had a thick, flat snout and a barbed tail that whipped menacingly from side to side. Multiple legs bunched underneath it as it readied itself to spring. Ready to attack. A sharp hissing noise came from its mouth. There was an energy coming from the creature. It felt familiar. Jonathan remembered the same feeling when he saw the blue haired boy from Pandemonium, but there was still something that connected this creature to him.

Jonathan gripped his knife, looking at this…thing. His muscles tightened, ready to fight and kill. It seemed that every instinct in his body waited for this moment. Finally.

The creature's many eyes bore into Jonathan's for some time, and sniffed the air with its snout before it bowed its head slightly, still keeping eye contact. Jonathan wasn't sure if it smelled something else on the ground or if it was something of more significance. All of its eyes looked at Jonathan again before it went back to searching for something.

Slowly Jonathan took steps away from the beast, moving silently as usual, knife still clutched in his hand.

His mother was gone.

Clary was not home.

Jonathan didn't know where he was going, but he wasn't staying here he had to find his family.

He left.

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	4. The Institute

Chapter 3: The Institute

Jonathan kept walking until he reached an empty alley. It wasn't far from home, but still far enough that the atmosphere had changed. There was a yellow streetlight buzzing above him and he still held his knife in his hand. In this area, at this time of night, he blended in quite well with his dark clothes and hoodie. The faint whine of police sirens echoed in the dark. Most people would be afraid to be alone like this at night, but Jonathan thought otherwise. He found peace here. He liked the way that people shut their curtains when he walked by, and the way they made sure to lock their doors. It made him feel superior and a threat to the mundane lives they led.

A soft summer breeze whipped his pale blonde hair into his face as he leaned on a dirty metal bike lock. He took his knife and scratched the chipping green paint off even more.

He shouldn't be here. He should be looking for his mother; even more, he should be looking for Clary to warn her from going home. Whatever was in their house was dangerous, and for whatever reason, it didn't attack Jonathan. The creature didn't disgust Jonathan as much as it surprised and captivated him. He knew from years of growing up and being taught what was "wrong", that most people wouldn't feel the same toward the beast. The whole ordeal was confusing.

It was the faint screech that brought Jonathan back to his feet. For a moment he thought it was someone in one of the nearby houses, and most nights he would have left it alone, but something in the back of his mind knew that this was different. He felt something then. Panic. Another scream.

_Clary._

It was Clary's voice. He knew it. He had grown up hearing her voice rattle on. How and why he could hear Clary even though he was practically a mile away was another curiosity, but Jonathan didn't question it.

He took off running. His arms pumped in the air, knife still in one hand. He ran past a few people, who shouted obscenities, but he never looked back, he kept running, faster and with more stamina than most.

Flashing blue and red lights of a police car made Jonathan slow down. His mother always hated what he did, and warned him about getting caught. They would lock him away and look at him like a freak. He hated the police for that reason, but also because they fought against the very thing Jonathan loved, violence and pain. Jonathan and the police did not mix.

As he snuck around the side of the house he saw two figures on the grass behind the rose bushes, hidden from view. A blonde boy—the attacker, most likely—was kneeling over Clary's limp body. Jonathan dove for the boy, knocking him over. They rolled in the grass some, Jonathan eventually pinned him down with his knife to the boy's neck. That is when he recognized him as the boy from Pandemonium. Jace.

"What did you do to her!?" Jonathan demanded. As one hand held the knife deathly close to Jace's beating artery, the other fisted the leather material of Jace's jacket.

"Saving her, you idiot." Jace struggled under Jonathan's strength and eventually managed to break free. He crawled back over to Clary's side.

Jonathan noticed that she was sweating, breathing in short, raggedy breaths, and her eyes were drooping. Clearly she was drugged. She turned her head to look at her brother, but she winced and moaned.

"I told you not to move," Jace hissed. "That Ravener demon got you in the back of the neck. It was half-dead so it wasn't much of a sting, but we have to get you to the Institute."

Jonathan looked at the boy with incredulous eyes. "A demon?" he said aloud. "You're joking,"

"Afraid not," Jace muttered. He slipped a strip of cloth that he had ripped from his shirt and wiped it under Clary's neck. A waxy film was smeared on it now.

"That thing… it talked." Clary was beginning to shake involuntarily. Jonathan crawled closer so that he could take her hand. "It said it was going to eat me." _If it wanted to eat you, then why did it just ignore me? _Jonathan thought.

Clary seemed to be talking to Jace casually, like they knew each other for longer than just tonight. Jace must have been the boy she saw at Pandemonium too, but what other times did they meet?

"Yes," Jace said nonchalantly, "but you killed it first."

"You killed that thing?" Jonathan asked.

Clary met her brother's eyes, confirming his question. Then her eyes filled with fear, "Mom—"

"I know." Jonathan whispered. He didn't know if he whispered because he didn't want to show the emotion that was in his voice or if he spoke softly for Clary's sake. He couldn't deny it. Right now, Jonathan felt vulnerable. There were too many things that were happening that were out of his control. His mother, Clary, and possibly demons? What was happening?

The feeling of not knowing what was truly out there, the unknown, being uncertain, the uncanny feeling that came over him every time he saw Jace and when he saw that monster; these were the things that were upseting Jonathan the most.

"I have to take her to the Institute." Jace's voice was serious.

"No." Jonathan helped Clary as she tried to sit up.

Jace's gold eyes met Jonathan's dark ones with fierce certainty. "She will die in an hour if I do not take her with me."

"What about the police, they can help," Jonathan knew if he talked to the police it would be risky for him, he might not hold his temper, but if it meant saving Clary then he would do it.

"They'll be no help. They're most likely demons too," Jace seemed bored as if he was repeating his story over again.

Both Clary and Jonathan looked through the bushes to see a policewoman holding a flashlight. They ducked under its beam as she searched, but as the officer turned they could see a fleshless, pointy, skeleton hand. Clary gasped. Jonathan seemed unmoved.

Jonathan looked at Clary and then to the new boy with the strange markings. "Fine, but I'm going with her."

"Fine," Jace glanced to the back of the house. "Can we get out through that ally?"

"No, it's bricked off. It doesn't make for a very easy escape," Jonathan said from years of experience of sneaking out.

Clary started coughing and put her hand to cover her mouth; it came away red. She looked at the two boys with worried eyes.

Quickly, Jace grabbed Clary's wrist, turned it over and took out a sharp and silver tool.

Jonathan grabbed his shoulder, yanking Jace away from Clary. "What the hell?"

"I'm helping her, idiot," Jace repeated. "If I'm right, which I always am, it will keep her from being seen so we can get her back to the Institute." Jace clenched his jaw. "Your sister has little time, now is not the time to be questioning me." It was apparent Jace was growing impatient; Jonathan was too.

"Do it to me first," Reluctantly, Jonathan surrendered his arm. Today was so twisted that trusting a stranger seemed like a normal thing to do.

Jace placed the tip of the tool to Jonathan's forearm and began to draw. There was a stinging sensation, but Jonathan didn't pull away. As soon as Jace stopped, there was an inked black symbol similar to the ones that covered Jace's arms and neck.

Without another word Jace began working on Clary and murmured something. _Covenant,_ it sounded like.

After that Clary passed out. Jace tried to catch her, but Jonathan pushed him away, scooping his sister into his arms. Her head bobbed over one elbow and her legs dangled over the other. "Lead the way," Jonathan said.

. . .

Clary lay on the white bed in the infirmary. Rows of empty metal headboard beds were lining the room. Linen sheets draped over her. It reminded Jonathan of the white cloths used to cover bodies on those criminal television shows. He quickly dismissed the thought. Clary had been getting better. Her breaths were deep and steady. She had been in and out for about three days now; Jonathan didn't sleep for any of them. Jace's friend came in and out of the room, checking on Clary, mumbling words to each other in the doorway. Alec and Isabelle Lightwood, he had been told, were siblings.

Clary made a soft noise and tousled slightly. Isabelle straightened. She was beautiful with dark black hair that had been braided and was casually wearing jeans and a tank top with a ruby pendant necklace. "So you're finally awake." Her voice was dry. "Hodge will be pleased. We all though you'd die in your sleep." Jonathan shot Isabelle a deathly glare. "Well, except for your brother, he stayed by your side the whole time."

"Is this the Institute?" Clary's voice was raspy as sandpaper. She struggled to sit up.

Annoyed, Isabelle responded. "Yes, and this," she spread her arms dramatically, "is the infirmary."

"How are you?" Jonathan asked.

"Achy," she timidly rubbed her neck. "And… hungry."

"Oh, I almost forgot," Isabelle went over to the counter to grab the tea that had been steeping. A soft steam rose from the pot.

"You've been sleeping for three days, you ought to be hungry." Jonathan tried his best to be comforting, to bring warmth and happiness in his voice. A smile. All of it was forced. He _was _happy that his sister was okay; he just couldn't show it how most people could. This was the way it had always been: a world of lies and pretending, but it seemed now that the world he knew was slowly crumbling.

Clary has finished sipping her tea and was staring questioningly at Jonathan, Isabelle too. "I swear boys are always off in their own world," Isabelle scoffed.

Apparently they had been talking when Jonathan was lost in his thoughts. "What did you say?"

"I said it's time for some girl talk and that I can take care of her the rest of the time. You can go sleep in one of the extra rooms or something, I don't really care." Isabelle said, shooing him away.

"But—" Jonathan tried.

"I'll be fine," Clary smiled. She made it seem so easy.

"Come get me if you need anything," said Jonathan. He had only known these people for three days, but they had treated him and Clary well. Plus there was that feeling, that uncanny feeling, which had always been tugging at him, that said they were different. Different in the same way that Jonathan was different.

There were numerous hallways in the Institute that would normally be like a confusing, intimidating maze for most, but Jonathan had memorized the path to his room. A left out of the infirmary, fifteen steps down, right, right and then the seventh door on the left. Twenty-three more steps and a right turn led him straight to the library, which is exactly where he was going. He couldn't be hold up in his room like a caged animal, he would go mad.

When he walked into the library he was instantly engulfed in the size of the room. There were countless books that lined the domed walls and tall ladders that spotted the shelves. Even though there were glass light fixtures, the library smelled like wax and dust. The wooden floor was dark and embedded with sparkling pieces of glass that reminded Jonathan of the familiar night sky.

In the center of the room was a desk. The desk was carved out of an entire slab of wood that was shiny with years of wearing. The slab on the desk seemed to be crushing two angels, their wings spread fruitlessly to try and ease the pressure off of their backs. Their faces held pain and suffering. Behind the desk was a weathered looking man with gray hair. He kept his eyes down, at his papers, as he spoke, "You must be Jocelyn's boy," It wasn't phrased as a question, but more of a statement. Jonathan tore his eyes away from the angels and to the man. "Although, your sister shares your mother's looks," The man stood up and held out a hand, "My name is Hodge,"

"So I've heard."

"How much have they told you?" Hodge asked, clasping his hands behind him.

"Demons, angels, shadowhunters, and downworlders. Basically everything that came out of my mother's mouth was a lie." In the infirmary Jace's friends would come in and tell bits and pieces of the shadowhunter world when they were tending to Clary. Jonathan's knowledge was still inconsistent, but one thing he did learn was that his mother was a shadowhunter once, which meant she had kept this world from him and lied about it everyday. That made him angry.

Jonathan looked at the struggling angels again. Seeing such hailed and powerful creatures in pain like that intrigued Jonathan and almost brought a smile to his face.

"Yes," Hodge nodded with a smile, "Jocelyn, she was like us you know,"

"It doesn't surprise me," Jonathan said with aggravation and then mumbled, "She's even more of a hypocrite than I thought."

"I take it you're not close with your father either?" Hodge asked. At that moment, a black bird flew in and perched on Hodge's shoulder. It cocked its head at Jonathan and cawed.

"My father died before I was born," It was a simple statement. It held no remorse; it was simply factual.

"A shadowhunter, like your mother, prestigious family." Hodge commented. "You look just like him,"

Jonathan made a noise that resembled a choke and a laugh, "hardly,"

"I beg to differ," said Hodge. "He has the same white hair, hard angles, and I bet you are as good of fighter as he is too,"

Jonathan glanced sideways at Hodge. "You make it sound like he's still alive,"

"That's because he is and he would love to meet you."

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**Sorry it took so long to update. I keep seeing people adding this story to their alert list which makes me happy, i'm glad you all are enjoy it. I hope you liked this one too. Review please! **

**sorry for any grammar errors.**


	5. Valentine

**sorry for the huge hiatus. i had spring break, and then crazy family issues, and then loads of homework on top of all of that, AND some writers block. since most of city of bones doesn't deal with sebastian/jonathan it's hard to come up with what is going to happen in this story.**

**this chapter begins with a flashback to the prologue, so if you think it would help to read it then i would recommend doing that ;D **

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Chapter 4:

_Luke's Lake House 1996:_

When Jonathan woke up the next morning there was a sliver of early morning sunlight coming through the laced curtains. He saw that his sister's small body was still sleeping in the bed across from him. Her chest rose and fell with slow deep breaths. For a moment he wondered what it felt like to be completely at peace like that.

Jonathan threw the heavy quilt off of him and padded to bathroom. In the oval mirror he could still see specks of blood on his neck from the deer he slaughtered last night. He could still feel the warm blood of the slain animal running down his hands and snaking down his arms. He had cleaned up most of the blood, but he could still feel its lingering presence. A sort of ghost of the thing he killed, but instead of fearing it, he embraced it.

As he walked down the stairs, avoiding the creaky areas, he heard voices. It was his mother and Luke speaking in hushed voices. Jonathan squatted down at the top of the steps and grasped the railing's poles as he listened.

"He did what?" his mother asked, appalled. Jonathan could hear the terror in her voice. Almost all of the memories Jonathan had of his mother were like this. Some part of Jocelyn was always afraid of her son.

"I caught him with a knife when he was coming in," Luke was speaking now. Jocelyn seemed to have gasped. "Don't worry, I went out to the woods, it was just a deer."

"But when in is it going to be something bigger than a deer? I can't even get Clary a pet because I'm afraid that her brother will kill it." Jocelyn paused for a long while and Jonathan thought that maybe this was the end of the conversation.

He didn't understand why his actions made his mother so upset; all he knew was that when she found out, she was frantic. He liked the uneasy tension that overwhelmed her. It made him feel in control.

He always wondered why he was different, why his mother had to remind him to smile because it was normal, why she had to force him to be nice to other children, why she had to tell him that killing deer was wrong. Why wasn't it normal? It felt normal to him; it felt good.

"I took him away from his father because I thought maybe, just maybe, I could keep the truth of what he is away, but now I see how futile that was. I thought I could prevent him from becoming a monster, but he is just like his father. He is becoming the exact thing his father wanted."

A monster.

That is what his mother really thought of him. A _monster_.

"Maybe you should tell him. It's eating away at him. Even with the help of Bane, his true nature is still scratching its way to the surface. Pushing down his darkness isn't helping. He is only going to keep acting out. If got the chance to see the hidden world, to fight—"

"No." Jocelyn's voice was tight. "It's just too risky. He can never know. I will never let him become his father."

. . .

_Present Day:_

Jonathan stood in the patchy, brown grass looking at the abandoned ruin. The wooden sign, just before the rusting fence, declared this was once a place called "Renwick's Smallpox Hospital". It was probably once an elegant towering building, but now it crumbled down to jagged, roofless walls. Apart from the rubble, there was nothing to see.

Hodge had said Jonathan's father was alive and that he was here. The only thing that could possibly be living here were rats. "I knew you were lying to me." Anger started to boil inside of Jonathan. "There's nothing here. My father's not alive." Jonathan began to turn around in annoyance. He actually believed someone—a stranger—_how foolish_. Any other day he would have beaten Hodge, but Jonathan had to return to the Institute before Clary noticed he was gone.

Hodge spoke up, "look closer," there was a strange smile in the tone of Hodge's voice.

Something caught in the corner of Jonathan's eye, making him stay. It was like a little ripple in water, starting in one place and then escalating out. The longer he looked, the more a different shape began to appear. A hidden building began to form, except what Jonathan was seeing was more like a Gothic castle. The lower level windows were darkened with shutters, but flickering candlelight still shone through. A pointed, arched doorway was at the top of a great stone porch. The entire structure was extremely compelling. _This building_, Jonathan thought, _is a place I could live in. _Dark, mysterious, and sinister.

"Shall we?" Hodge guided Jonathan toward the looming castle. He didn't look back to see if Jonathan was following him. The raven that had been perched on Hodge's shoulder flew ahead and disappeared in the building.

Inside, the walls were lined with flickering torches and the granite architecture mimicked the grandeur of the outside.

Hodge led Jonathan along the long, empty corridor and their footsteps clicked against the hard floor in synchronization. Jonathan was still skeptical of Hodge, but decided he wasn't completely wasting his time. He did like looking at the gothic hospital. Its eerie, haunted, abandoned feel seemed to call to Jonathan. If anything, this building felt more welcoming than Jonathan's real home had ever been.

Hodge stopped abruptly in front of a tall, dark wooden door, opening it. As it opened, the raven came by and flew in right past Jonathan's head. _Damn bird, _he muttered.

Jonathan thought of the times he used pebbles and a slingshot to shoot birds out of the air when he was young. Clary always went to her mother, crying for him to stop, but he kept shooting them with a grin on his face. He could still see the worried frown on his mother's face.

Hodge opened the door to a dark room, lit only by a fireplace. There were red velvet drapes that cascaded to the floor and the room was empty apart from a wooden desk, a mirror, and a man at the desk with his head turned to look out the window at the moon lit field. A thin layer of dust seemed to have settled in every crevasse.

"My lord Valentine," Hodge started. The man at the desk raised a hand but did not turn his head to look at his guests. He gaze remained out the window, to the moon.

"That is all, Hodge," the cryptic voice ordered and Hodge shuffled out of the room. Jonathan heard the door close behind him.

The man behind the voice stood. He was tall and muscular. Angry white scars covered his hands. This man, whoever he was, was a fighter—a lethal one at that. The man's hard angled eyebrows sloped into his dark, black eyes. His silver hair was clipped close to his skull. He was wearing all black, leather, with a large sword sheathed to his belt, nothing ordinary about him whatsoever. "Jonathan," the man's lips curled into a grin. "There are so many things you need to know, so many things your mother hid from you."

"You are my…father?" The word didn't seem right coming out Jonathan's mouth. He looked at the stranger, _really_ looked at him. He had to admit, they did share common characteristics. This man _could_ be his father.

Jonathan thought of the other man that was framed on the fireplace mantel, the man he had always thought was his father, the man he had never felt a connection with.

"I am," the man, Valentine—as Hodge had said earlier—walked closer to Jonathan. "I have so much to teach you."

"Then start with all of this. What the hell is going on? And if you are really my father, why am I just meeting you now? Why has my mother been lying about everything?"

"Your mother is weak. She wasn't at first. She was an excellent fighter and Shadowhunter, but she grew weak." Valentine's spoke the words with disgust.

"My mother," Jonathan was shocked. "Was a Shadowhunter? She fought demons?"

Valentine nodded his head slightly. "She did, along side with me. We fought demons and downworlders—vampires, werewolves, fairies, and warlocks."

"Then why keep all of this a secret? Why lie? This world is amazing. It has amazing beings and amazing powers."

"Because she is weak." Valentine repeated. "She found out what you are and she took you away, stole all of the opportunities we could have had together. She kept you in the dark about this world because she is afraid of it. She thought I would raise you to be a monster. She has no idea of the greatness you have."

He took in Valentine's words and decided that he agreed with them. He remembered overhearing the countless conversations that Jocelyn had fretting over her son, the countless times he had heard her call him a monster.

Jonathan always felt distant from his mother. He was always stronger too (in all senses of the word). She would cringe around her son when she thought of the things he liked to do. "You said she was afraid of what I am, you're talking about something other than a Shadowhunter, aren't you?"

Valentine took a breath, the sort of breath you took before beginning a long story. "Shadowhunters were created when the angel Raziel shared his blood with a mortal, creating a breed that was strong enough to fight off demons. Shadowhunters are half-angel half-human, but you," Valentine smiled. It wasn't a normal smile, but the smile of a twisted mad scientist inspecting his creation. "You, are so much stronger than they are. You not only have angel blood, but demon blood as well."

For a moment, Jonathan was disgusted. He remembered the thing—the demon—that was in his house, how it attacked Clary, but did not attack Jonathan. He remembered how the demon seemed to bow before him. The more he thought about it, about having demon blood, the more he realized what an incredible gift it was. He was stronger and faster than all of the Shadowhunters. They were weak and he was superior. Jonathan's cruel smile mimicked his father's. He had only known this man for a few minutes, but he felt more connected with him than with his actual family.

"When your mother found out what power I gave you, she was appalled. She took you away from me. She separated us. She said that I would make you into a monster. She said that _you_ were a _monster_." Valentine practically growled.

Jonathan curled his fists at the thought of Jocelyn's selfishness. He had a father this whole time. She kept him away from his father this whole time. There was world so much greater than the one he knew and she kept that away too. Jonathan never had a choice in the matter and for that, he hated his mother.

He was strong. He could fight. He could _kill_.

"She stole so much from the both of us," Valentine continued. "She has something that I need, and I need your help getting it."

"What is that?" Jonathan asked, ready to do anything.

"The Shadowhunter that summoned the angel was given a cup, a sword, and a mirror by the angel—the Mortal Instruments." Said Valentine. "Your mother has stolen the cup."

"Why do you need the cup?"

"Let me worry about that," Valentine wicked grin appeared on his face again. "What I need from you is to keep those Shadowhunters busy and out of our way. You will tell me their every move. In the meantime I will train you, and you will finally reach your potential." Valentine had his hands on Jonathan's shoulders. If Jonathan could feel happiness, he would feel it now.

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**hope you guys like this still :) REVIEW PLEASE!**


	6. Magnus Bane

**_super sorry for the long hiatus... so, i'm thinking about starting a new fanfiction which means this one may not be updated as much.. plus i don't really have specific ideas of what to do in chapters after this other than developing this Jonathan into Sebastian by the end of the story.. so if you have a goo transition from point A to point B let me know... please review and let me know how i am doing_**

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_Chapter 5: Magnus Bane_

The blood was warm on Jonathan's hands. The werewolf was dying quickly, gargling its last words; Valentine hadn't given him orders to do this, but it felt right; it felt like it needed to be done. The unnatural Downworlder needed to be killed. Jonathan was simply taking out the trash and he knew Valentine would have wanted this.

Valentine had explained everything about Jonathan's mother and Luke. Valentine told him the story how Luke (Lucian as he was known back then) had been closer than brothers, a pair of warriors, _parabatai. _He told Jonathan of how he fought alongside Herondales, Graymarks, Lightwoods, Waylands and Fairchilds. How he created 'The Circle' and hoped to rid the world of the awful Downworlders. How Valentine and Jocelyn were married, how Valentine fathered Jonathan and Clary. Jonathan learned that Luke had been attacked by a werewolf and therefore turned into one and that Luke was now the head of a pack here in New York.

_All this time I have been lied to… by everyone. _Rage filled Jonathan and he curled his fists until his skin turned white.

"The Uprising was a disaster." Valentine's voice was disappointed. "The Circle attacked during the Accords when Downworlders come to Idris to sign a peace treaty. It was a disaster—no one listened to orders. In the end Hodge was exiled to the New York Institute, and the Lightwoods were sent there as well with their children. I was forced into hiding, and eventually had to fake my own death in order to pursue my work in peace."

"How are you going to find the Mortal Cup. You said Jocelyn had it. She is gone now." Jonathan questioned.

A smirk that reminded Jonathan of a predator came upon Valentine's face, "And who do you think has her?" Jonathan said nothing, but understood. Jocelyn was here. Valentine was the one who had come into his house. "She has answers, but she has locked them away inside her head. It will take much time to find them."

Valentine lifted his hands and cupped them around Jonathan's jaw. There was a rune on the back of one of them that looked like an eye. He had described that it was a voyence rune. "This is why I need you. You are an extension of me. You must continue my work while I search for the cup inside Jocelyn's mind."

_Continue my work…_ The words buzzed in Jonathan's head as he lifted the head of the bleeding werewolf. Its breaths were short and jagged, and fear filled its eyes. Its bottom lip quivered as it mumbled a last prayer. Funny, it had been fighting and growling for its life before, it even scratched Jonathan, but now it welcomed death. Jonathan lifted his sword one last time. The blade came down on the werewolf's neck.

Silence.

. . .

"What," Jonathan paused, eyeing Clary's peculiar outfit. "Are you wearing?" Jonathan certainly wasn't one to know or judge fashion, but this outfit was ridiculous. His sister was wearing a pair of jeans that were rolled several times at the ankle and a shirt that exposed too much flesh around her chest. Where the pants were long, the shirt was tight. On any other girl, Jonathan would not have minded the cleavage, it was hot, but this was his sister.

"That bad?" Clary winced and looked down at her clothing.

Jonathan had left his father at Renwick's. Over the past few days Valentine instructed him on everything, and taught him complicated sword fighting (which he picked up easily). He had trained all night with his father, maybe even a day or two (time seemed indefinite at Renwick's). He had told Clary he was picking up clothes for her and that he would be a while. She believed him. _Of course she did_. She is as gullible as their mother.

Since Jonathan had been spending time with his father, his mind had become clearer. He could remember everything. The Downworlders at Pandemonium and the warlock with the cat eyes he and his sister were taken to every few months—the warlock that _stole_ their memories under his _mother's _command.

Jonathan frowned.

"What is it?" Clary asked.

"Nothing," Jonathan replied.

Still picking at her clothing, Clary continued talking, "The clothes are Isabelle's. She lent them to me. Did you bring extra for me?"

Jonathan handed Clary the duffle he had retrieved from the house.

He thought of what his father had told him. The Lightwoods were a few of the many who worked with Valentine at one point, and later had three children, Alec, Isabelle, and Max. Jonathan had asked why Valentine was not working with them still but he had replied, "They think I am dead. Which is the way it should be if I want any of my plans to work."

"Jonathan!" Clary practically had to yell. His only response was an interested hum and an eyebrow raise. "Jace and his friends are taking me out to eat, now that I'm feeling better and know everything. Do you want to come?"

"No. I'm not hungry." Jonathan let his mind wander back to his father and his training. "Wait, what do you mean 'now that you know everything'?"

"They took me to the Silent City." Clary clenched her jaw, clearly agitated. "Mom kept this whole world from us, Jonathan. A block was put on our minds. Jace said a warlock did it."

Since training, Jonathan's mind had become clearer. He could remember visiting the warlock with the cat eyes. Magnus Bane. He was the one who stole his memories; he was the one who took his thoughts and hid them away, and worst of it—as if being mentally robbed by a _warlock _wasn't bad enough—his own mother gave the orders.

Valentine had said the spell wore off faster with Jonathan because the demon blood made him stronger and harder to manipulate. Clary on the other hand was easier to fool, however they both wore out the spell eventually.

"So what are you going to do?" Jonathan asked his sister.

"Well, like I said, we're going to eat, and then figure out what's next."

"CLARY!" Jace's voice echoed through the Institute's massive hallways. It sounded like he was downstairs.

Clary rolled her eyes. "Are you going to come or not? They're waiting for us."

_I want you to watch them, figure out their next move._ Those had been his father's words. Jonathan had to infiltrate these Shadowhunters so that they did not catch on to Valentine's plans. Jonathan curled his lips. "I am coming."

. . .

Taki's, the so-called restaurant, looked like it was about to melt into the ground. When Jonathan reached for the creaking door he thought it would disintegrate in his hands. A judgmental sneer crawled onto his face. "I honestly don't know what I expected."

Taki's was a restaurant for Downwolders of all sorts, and (apparently) Shadowhunters too. A group of rather large teen werewolves were congregated at a booth, tearing at a chunk of red meat with their teeth, oblivious to the silverware provided. (They also could have been avoiding the utensils due to the likelihood of it being actual silver, but by the looks of the run-down place, Jonathan didn't think that was the case.) Next to them was a woman with translucent wings and hair that was the same pale green color and texture of Spanish moss. The faerie was talking to a man with blue dreadlocks. "Is that a demon?" Clary asked.

_Of course not_, Jonathan answered in his head. By now he could successfully label every type of Downworlder, thanks to his father. "It's an ifrit. They are warlocks that have no magic." Jace responded.

Jonathan followed Jace, Clary, and Alec into a booth. Sitting uncomfortably between Alec and Clary, Jonathan stared at Jace from across the table. Jace was too busy explaining something to Clary to notice, but Jonathan observed his every move, stalked him like prey. There was just something about him, his quirks, the way he walked, his posture… there was something Jonathan could see in it that made him wonder, but he couldn't figure out what. What was it about this boy that seemed so familiar?

"Hey!" a female voice called out as she climbed into the booth—Isabelle. Following close behind, like a puppy, was Simon. "Did you guys order yet?"

Taking that as a queue, Jonathan lifted his menu and read. Some of the foods consisted of fried mouse-tail, locusts and honey (the special), a variety of raw meat, and several different types of animal blood on tap.

"Nope," Alec replied.

"Good," Isabelle said with a smile. "I'm craving my apricot-plum smoothie." Quickly forgetting about her craving, she asked. "How did it go at the Silent City?"

"We have a name, Magnus Bane—"

"Isabelle, what did you say was good?" Jonathan interrupted, trying to get them off the subject. Sure, it was a lame attempt, but it was the only one he could think of in short notice.

They all looked at Jonathan with bewilderment, Isabelle especially. "I—ah, didn't say anything. I just said I wanted a smoothie. Oh, and stay away from the faerie food," she eyed Jace for some inside reason and looked back to Jonathan. "I make no promises of what the effects may be."

"Oh, yes," Jonathan nodded. He waved over the waitress. "We are ready to order over here."

The girl came over obediently. From the back, she was a pretty blonde, with a curvaceous ass, and it was only when she turned around that Jonathan could see her fault. She had all blue eyes, no white, just blue and when she smiled she revealed sharp little teeth. Her nametag, located on the round of her breast read Kaelie. "What can I get for you?"

"I'll have the smoothie," Jonathan handed her his menu.

The others still looked confused by his behavior, but ordered anyway. "I'll have the smoothie as well," Isabelle chimed. Clary and Simon ordered coffee. Jace looked over the menu one last time before grunting and then adding, "I'll have the usual."

"Me too," Alec added.

Kaelie finished scribbling her notes and replied, "coming right up".

"Was she a ifrit too?" Clay whispered, even though the girl was out of hearing range.

"Part fey I think…" Jace was playing with one of the knives provided at the table.

"Nixie," Jonathan murmured.

"I'm sorry what was that?" Jace set down the knife—not lightly—back on the table, obviously irritated with Jonathan.

"Nixie. She has nixie eyes—all blue like that." Again, the look of confusion appeared on all of their faces. "That book that you have that teaches you everything, that training manual…" Jonathan left his thought hanging.

"The Shadowhunter's Codex?" Alec helped.

"Yes, the Codex. I read it."

"Well, congratulations." Jace retorted sarcastically.

Kaelie came back shortly with their meals and they began to eat. Jonathan kept quiet, not drinking the smoothie he ordered and just observed. Jace mostly was explaining the uneasy relationships between some of the Downworlders and Shadowhunters. "We stand them and they stand us, for the most part."

Jace concluded. "I enjoy the company of certain Downworlders from time to time. But we don't really get invited to the same parties."

"Wait," Isabelle interrupted, suddenly digging her hand into her purse and fishing out a flyer. "I knew that name sounded familiar. Magnus Bane, High Warlock of Brooklyn." Isabelle turned the flyer around for the others to read. It was printed on thin paper, nearly parchment, in a thin, elegant, spidery hand. It announced a gathering at the humble home of Magnus the Magnificent Warlock, and promised attendees _"a rapturous evening of delights beyond your wildest imaginings."_

"So, I guess this means our next stop is a party." Jace announced.

For being who he was, Jonathan wasn't doing a very good job at keeping the Shadowhunters away. Every step they took to find the secrets locked in Clary's head was another step closer to finding her real father. Valentine.

Jonathan had to do something to stop them—slow them down at least, and he had an idea.

* * *

**please review. i haven't been getting many on the past chapters so i am wondering if i should just let this one go and start my new fic (which will be in vampires and not TMI)... but please let me know your thoughts :)**


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